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- PDB-8dsb: Lambda Bacteriophage Orf63 -

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Basic information

Entry
Database: PDB / ID: 8dsb
TitleLambda Bacteriophage Orf63
ComponentsXis (Excision72)
KeywordsVIRAL PROTEIN / BACTERIOPHAGE / LYTIC DEVELOPMENT
Function / homologyBacteriophage lambda, Xis (Q38267) / Protein of unknown function (DUF1382) / viral capsid / Xis (Excision72)
Function and homology information
Biological speciesLambdavirus lambda
MethodSOLUTION NMR / simulated annealing
AuthorsDonaldson, L.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2018-05838 Canada
CitationJournal: Front Microbiol / Year: 2017
Title: Bad Phages in Good Bacteria: Role of the Mysterious orf63 of lambda and Shiga Toxin-Converting Phi 24 B Bacteriophages.
Authors: Dydecka, A. / Bloch, S. / Rizvi, A. / Perez, S. / Nejman-Falenczyk, B. / Topka, G. / Gasior, T. / Necel, A. / Wegrzyn, G. / Donaldson, L.W. / Wegrzyn, A.
History
DepositionJul 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xis (Excision72)
B: Xis (Excision72)


Theoretical massNumber of molelcules
Total (without water)17,7162
Polymers17,7162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALS was performed at the SPARC Centre at the Hospital for Sick Children (Toronto, ON) to confirm the dimeric assembly.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area5770 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Xis (Excision72) / orf63


Mass: 8857.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lambdavirus lambda / Plasmid: pD441-NH / Details (production host): ATUM Electra Vector / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q38267

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D 1H-13C NOESY
151isotropic13D 1H-15N NOESY
1121isotropic13D C(CO)NH
1111isotropic13D CBCA(CO)NH
1101isotropic13D HN(CA)CB
191isotropic13D HNCA
181isotropic13D HN(CO)CA
171isotropic13D HNCO
161isotropic13D HN(CA)CO
1151isotropic13D (H)CCH-TOCSY
1141isotropic13D CCH-TOCSY
1132isotropic23D 12C-filtered 13C-edited
1161isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution15 mM TRIS, 140 mM sodium chloride, 0.05 % w/v sodium azide, 0.8 mM [U-98% 13C; U-98% 15N] sample, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution25 mM TRIS, 140 mM sodium chloride, 0.05 % w/v sodium azide, 0.8 mM [U-98% 13C; U-98% 15N] sample, 90% H2O/10% D2O12C13C_sample90% H2O/10% D2O1:1 mixed sample to obtain intermolecular NOEs
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMTRISnatural abundance1
140 mMsodium chloridenatural abundance1
0.05 % w/vsodium azidenatural abundance1
0.8 mMsample[U-98% 13C; U-98% 15N]1
5 mMTRISnatural abundance2
140 mMsodium chloridenatural abundance2
0.05 % w/vsodium azidenatural abundance2
0.8 mMsample[U-98% 13C; U-98% 15N]2
Sample conditionsIonic strength: 140 mM / Label: main_conditions / pH: 7.7 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7001York University
Varian INOVAVarianINOVA6002University of Toronto

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RosettaBakerrefinement
CYANAstructure calculation
Refinement
MethodSoftware ordinalDetails
simulated annealing3100 structures chosen from 5000
simulated annealing420 structures chosen from 100
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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